1NM6

thrombin in complex with selective macrocyclic inhibitor at 1.8A

• PDB DOI: https://doi.org/10.2210/pdb1NM6/pdb

• Classification: BLOOD CLOTTING/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Hirudo medicinalis
• Mutation(s): No 


• Deposited: 2003-01-09 Released: 2003-09-02 
• Deposition Author(s): Nantermet, P.G., Barrow, J.C., Newton, C.L., Pellicore, J.M., Young, M., Lewis, S.D., Lucas, B.J., Krueger, J.A., McMasters, D.R., Yan, Y., Kuo, L.C., Vacca, J.P., Selnick, H.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.216 

Literature

Design and synthesis of potent and selective macrocyclic thrombin inhibitors

Nantermet, P.G., Barrow, J.C., Newton, C.L., Pellicore, J.M., Young, M., Lewis, S.D., Lucas, B.J., Krueger, J.A., McMasters, D.R., Yan, Y., Kuo, L.C., Vacca, J.P., Selnick, H.G.

(2003) Bioorg Med Chem Lett 13: 2781-2784

• PubMed: 12873514 
• DOI: https://doi.org/10.1016/s0960-894x(03)00506-7
• Primary Citation of Related Structures:  
  1NM6, 1NT1


• PubMed Abstract: 
  

  A series of potent and selective proline- and pyrazinone-based macrocyclic thrombin inhibitors is described. Detailed SAR studies led to the incorporation of specific functional groups in the tether that enhanced functional activity against thrombin and provided exquisite selectivity against trypsin and tPA. X-ray crystallography and molecular modeling studies revealed the inhibitor-enzyme interactions responsible for this selectivity.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.02 kDa 
• Atom Count: 2,562 
• Modelled Residue Count: 287 
• Deposited Residue Count: 298 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thrombin	A	287	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hirudin	B	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28504 (Hirudo medicinalis) Explore P28504  Go to UniProtKB:  P28504

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L86	C [auth A]	(11S)-11-BENZYL-6-CHLORO-1,2,10,11,12,13,14,15,16,17,18,19-DODECAHYDRO-5,9-METHANO-2,5,8,10,13,17-BENZOHEXAAZACYCLOHENI COSINE-3,24-DIONE C27 H33 Cl N6 O2 LYVSCNRRXJZCRV-QHCPKHFHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS	B	L-PEPTIDE LINKING	C9 H11 N O6 S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
L86	BindingDB:  1NM6	Ki: 0.09 (nM) from 1 assay(s)
	PDBBind:  1NM6	Ki: 0.09 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.216 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.7	α = 90
b = 71.4	β = 100.5
c = 72.3	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-02 
Deposition Author(s): Nantermet, P.G., Barrow, J.C., Newton, C.L., Pellicore, J.M., Young, M., Lewis, S.D., Lucas, B.J., Krueger, J.A., McMasters, D.R., Yan, Y., Kuo, L.C., Vacca, J.P., Selnick, H.G.

Revision History  

• Version 1.0: 2003-09-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary